Dillon Passage tied the knot with the Netflix star in December 2017, before he was arrested on charges of animal abuse and orchestrating a murder-for-hire plot against a rival.
Joe, whose real name is Joseph Maldonado-Passage, is serving a 22-year federal prison sentence for trying to have Big Cat Rescue CEO Carole Baskin killed.
His downfall featured in Netflix’s wildly popular docu-series Tiger King, which premiered in March last year.
Dillon announced on Instagram he has split from Joe but promised to “always love and support him”.
After describing being thrust into the spotlight due to Tiger King as “incredibly uncomfortable,” he said: “To answer the main question the public wants to know, yes, Joe and I are seeking a divorce.
“This wasn’t an easy decision to make but Joe and I both understand that this situation isn’t fair to either of us. It’s something that neither of us were expecting but we are going to take it day by day.
“We are on good terms still and I hope it can stay that way. I will continue to have Joe in my life and do my best to support him while he undergoes further legal battles to better his situation.”
The couple’s wedding came two months after the death of Travis Maldonado, Joe’s previous husband. He accidentally shot himself.
In January Joe, who presided over big cats at a zoo in Oklahoma before he was jailed, was omitted from a list of pardons by outgoing president Donald Trump.
His legal team had been confident of securing his release after launching a high-profile campaign to capture Trump’s attention.